The exit status of the task that caused the workflow execution to fail was: 143.
The full error message was:
Error executing process > 'callVariants (23)'
Caused by:
Process `callVariants (23)` terminated with an error exit status (143)
Command executed:
#!/usr/bin/env bash
# Convert the list into a string separated by spaces
bedString="/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bf/c420875f5438a36765cbb0665f29b0/STAT1_STAT1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cd/214d0e062bed01fa73e7bf77f946bf/PKNX1_PKNX1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/aa/58dde70fea83f737b79d3c2d19d044/ELF3_MA0640.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ed/ca841128f4722f03ff8ca398010d7d/FOXK1_M08120_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/0d/7441e931980abd6627c0ecf3a6bec6/TCF7L2_M08167_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/df/eebfd7bbaaf6f2ffd5c800806acc37/ELF1_ELF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed 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/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/05/b475f9f047288adbd7f0dad62e4cf1/ZNF250_M08370_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/56/2cccbb647e292fbb2a355a7e36ca6a/ZNF200_M08273_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a4/b5244045ceac8d519f93aac8a61a2d/ZNF85_M08295_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/38/0a821a7c31b2de84054449b1b4cb9d/ZNF17_M07681_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a3/9744071b08218087d4131a0812a785/KLF7_MA1959.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/34/95a099f54bab380a033cfeb2c5ce15/MYF5_MA1641.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/62/e68e4a77763fab7ccc2e9533b1c240/ZNF587_M07746_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a9/9da2922e2839412f4956c3bc90afe6/ZFP42_ZFP42_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9a/f52bb5e3fc59ef002f398af255fbdf/ZNF202_M07612_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cb/9307eea5f6ada3d0ec220441b9f9ad/ZFP57_MA1583.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5e/9a4cf7ab068c93e44734f58bbc360c/ESR1_M08217_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b4/f044e0435c8a30f45ad535ccc5d19d/PAX5_M07996_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e0/b6a65c80351122f0b8d912dd6f4e6d/FOXQ1_FOXQ1_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c9/453c85e6238befe2bf2e7c6d8dc93c/SOX10_SOX10_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f8/b14cbf2e866a582705b4bc4382baa6/ZFP3_M08258_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/92/4278082b2d812dfffc55d9750aaddc/EGR1_MA0162.4_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7e/bb2c1d4883ad00cbac313ffe64d4fe/ZNF2_M07780_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/68/93e829548f02678343a5c5b49e1cfc/PATZ1_MA1961.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a3/011172ae0a99f43e86e72029f5a7da/ZNF84_M07736_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/6e/dbe2ec5e163a77601f7ec449bfa4a4/ZNF431_M07711_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/63/c55bce33458869e46320eefec097f1/ZNF766_M07699_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/22/0955305e2fa889423c45b52629fc9f/POU2F2_M08140_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9c/796b5811690cf85265f7134e401779/ZNF85_ZNF85_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ed/3ffa99f8bfe850d343968b5b1e53f9/JUND_M07816_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4d/a33f5c1f93fc05fce31f881d2dc3cf/ZN331_ZN331_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4f/26798388462562130ea8442db580ae/RFX5_M08011_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/58/6ea983b88c684bc382187507b212ce/EPAS1_EPAS1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/15/78a28383692f3c40465ebd3de4a46c/TP73_M08036_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/97/3e33cb1f633c411bc0acfcb3120954/ZNF320_M08362_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/90/0c4876cc5ca7d4ae8357bd1c1c1a9d/NR4A1_M08153_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/2c/0e40b729636cb9ff838526a4f13b3a/ZEB1_ZEB1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1d/bd0ec3667fe1e47c79789f605c5e73/ATF3_M07825_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e3/23911dc5e4164db378dbf12e744b5c/ZN350_ZN350_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/99/f188e65ae8937db26d77d8c0f808dc/SP2_M08326_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/db/20e6ab1f213b9bb6a3937d283071bb/ELK1_ELK1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3e/1be89429e046154d70e079cb6632e2/STAT6_STAT6_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/87/0deddef7ec6edc879bf97a8befafca/ZNF765_M07701_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/04/ca5f0b4e180b8ff4245e0cbee69e17/IRF1_IRF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fa/2f11a07dc67c6b881b2e206d8554e3/GATA2_MA0036.3_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/31/98803461d326046da90d5aa098a0ab/KLF9_KLF9_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/34/46562d928390e8f6f9474ec1e31b20/ERR2_ERR2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/63/9c6591b928ae574f6300e9159ce3de/CTCF_M07898_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/6c/33ebe520790a0c1fe1f9476dbb311a/BACH2_BACH2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/36/139a5c6d27425566669ec9bed631ce/CTCF_M08289_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/51/3dd090545a07bb21b70b5993265666/IRF3_IRF3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/79/8b7f44feffc087528a112c656445a7/ZBTB33_MA0527.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/35/b8270e0814460a6a69ad682a4e3e46/PBX1_PBX1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9a/12cdca4ef2637ae2d6ee9e2691fbbf/NANOG_NANOG_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b4/50c3c6e08de0bb205f7679ff2f96bb/FOXP1_M08115_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1f/11afe2413e48f6e89256b8134095be/ZNF334_M07740_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/02/722afa5b0ed7989e773e25641e866c/MBD2_MBD2_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/03/4b57f0ecaf509e2fde6ec3fe2fdf75/BHA15_BHA15_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a4/614ab92946ea1ec41169e0c0b848b7/ZNF528_M08328_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d4/0103e3346fe11cbdc363c247cdee12/ZNF662_M07666_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d1/460a6853d083e5f0802584814668cb/STF1_STF1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/33/dbbdcc4062d7571f34e4db9080edae/ZEB1_MA0103.3_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c8/7cbf6bf875240d1797629b520955a9/ZNF782_M07706_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/69/8c2ba78c65f2259aca9bfce0aa84fd/AIRE_AIRE_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3d/35700df8af29918599a1645ce17216/TF65_TF65_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b2/1b933bca329be3d6dacf4005d66df5/CTCFL_CTCFL_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/0e/f35809b34bad92ae87288f1793a109/ELF5_ELF5_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/46/c9959df71235e081db454d60224cdb/ELK4_M07958_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/12/5a253f5f72285c40d712f478ccf976/ZNF90_M07761_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e9/a291b909cc7f66c890ea50587e00b0/CTCF_M07888_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/28/d03f9977faf808bb1187cf43c6e87d/ZNF274_M07934_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/37/3db3e256acb68334c41d8ed952d650/JUNB_M08070_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3a/e974b12db7eeae5e11f42b2a7ff353/HXB13_HXB13_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c1/6065edd6961c5ecd92eab0369975a9/SMAD3_SMAD3_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f2/bfb7ec6f5b0154ea9766d6125fdfc9/USF1_M08056_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8b/d1daa02572f90eaa641e8e89bcb2f8/ASCL1_M08055_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fa/b755928e94b412aca66f849ba7505b/GRHL2_GRHL2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c4/b69ab0899c6d880cc58dca6a5e915b/MYOG_MYOG_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1c/be67fb1285640b5caff97f2cac2548/ZN140_ZN140_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed"
# Split the string into an array in bash
IFS=' ' read -r -a bedArray <<< "${bedString}"
# Count number of elements in array
echo "No. of BED files: " "${#bedArray[@]}"
mpileup_module() {
local BEDFILES="$1"
local BAMLIST="$2"
local DATAID="$3"
local FASTAFILE="$4"
bash /mnt/runParallelMpileup.sh "$BEDFILES" "$BAMLIST" "$DATAID" "$FASTAFILE"
}
# export function to be used in parallel
export -f mpileup_module
# determine the number of available CPU cores
num_cores=$(nproc)
echo "Number of cores: "$num_cores
# set arguments
bedFileArray="${bedArray[@]}"
bamPathList="X4RG73R.bamlist.txt"
dataID="X4RG73R"
# Use GNU Parallel to run the commands in parallel using all available cores
parallel -j "$num_cores" mpileup_module ::: "${bedArray[@]}" ::: "${bamPathList}" ::: "${dataID}" ::: "/refs/GRCh38_no_alt_GCA_000001405.15.fasta"
Command exit status:
143
Command output:
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/80/a8107b9e554a937aa9316ab54c771c/FOXH1_FOXH1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d9/93db57b71356384efcc24bda3a50d9/PPARG_PPARG_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/66/7ae80376c10ae992613da000b7053d/THA_THA_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/36/2060cf85de9da4084fa9611606fd57/PBX3_M07971_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/93/251ef1907cc6e5d4b28be1543c0a51/ATF3_M08188_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/15/847eaebe54c1ea6d1b5dcd99bccead/MAFF_MA0495.3_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/44/5ddf8f2aea106d9f02c4c39aa1e4e1/ALX1_ALX1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c0/a670593557297b2150e6359819f3ac/ZNF75D_MA1601.2_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/24/5c8808d33b0309eb038dd0d3845223/DUX4_M08135_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/15/56271ebc6bbea3875c5092fd4f864a/ZFX_ZFX_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/4c/3a1172a1ea4a8cc9ed2d15ea1ee9ea/NR4A1_NR4A1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1d/26a73e864c698400bee227a2a90590/ZNF621_M07636_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/61/cc4cf3148b55fc4e6a694b1a807470/MEF2B_MEF2B_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/fc/b42872310c3554208ebc3d4c26fdc1/TBP_M08231_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ef/3dadf9167af89526a1a8af79424c4c/KLF1_KLF1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d6/fb3f8455dbd580ab4b5f0e7b4e492b/ZNF653_M08248_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/66/92eefe074a6eb380cff9474882f26a/ZNF528_M07617_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/6b/fb316cd04959326c24b28e9dbf845c/ZIM3_MA1709.1_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a3/7735d11cd51fc88ac3cd8f359ec962/HLF_MA0043.3_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c8/925331c8fbd7f5776c13155e981a75/CTCF_M07901_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/24/accfa7e861ac472956b1956eb0ea73/MYC_M07803_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bf/64604e9f56663a47bc1d576656f40c/ZNF682_M07718_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5c/53b1654ad226eb2d3a8b3d65f00d5b/ZNF585A_M07713_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/92/0b7cb9d07cd2e097225f046603b020/KLF5_M08086_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/60/dbe1e369ec3e7ec45e3ef54d59d796/ZNF135_MA1587.1_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/94/f11445afa57052a50cff1c6c5427cc/SP2_M07932_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e5/57ece315d4827e854c8ab37ee07e88/RXRG_RXRG_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/35/02c41cec45ecb9536952ea8d05502d/ZFP69_M07686_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/85/a1147d2aa7c5fc83e24f1900e7ff71/PRDM9_M07610_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8b/e3bb3e88064830f2428c2497eeb849/DBP_DBP_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b1/cdb3afc99f3b678cb0634897ea70c4/MXI1_MXI1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/48/02b5e2ec38daa6d266a3973e1573d2/ZBTB7A_M07937_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8b/bf4f1fe6ff9665f449fa1192ca8f94/ZFP14_M07592_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e7/d75fa06f3424320cf5022981f85478/ZNF737_M07768_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/82/69daaa2d154f8f770197c9fe40b538/CTCF_MA1930.1_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e9/105dcb713e290cec359ea7608c48c5/ZNF33A_M07695_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/cf/32d769cd2d59c9de308638aa7b906a/HNF4A_HNF4A_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/1b/86c52425a134b7704ee797913d7cf8/NFYA_NFYA_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/23/7301b3f6f68f9e46b541b0811d4296/FOXO1_FOXO1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/89/076eb99d39c4f4b6a808810cac355a/ZNF667_M07737_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/02/d2e02d66dce653ccc0e08def6eec53/E2F6_M07939_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/bf/a714a833de56603e8b4fcc88eeea96/NFYA_MA0060.3_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3c/67967cac0538b8c0239dc0c91953f5/ZNF595_M08400_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/0f/17c680960372ae08d31145529811dc/STAT3_M08172_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f5/e1294639c33d39ac948837d6b6028d/ZNF317_MA1593.1_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/22/ec5aab798966276128923c0d08f37a/USF1_M07811_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7a/d46dbb9630cbcfb1a1113df2dbd0e1/GATA2_M08125_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/53/329614faece54eaf86133afc01795a/KLF7_M08298_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/aa/39bdda47d3a3dc6343eefbadbf5194/JUND_M07814_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Parallel job to execute with mpileup: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c5/72630e67b7a23c15fd5dfd84851795/CDX2_M08131_2.00_TOBIAS_TF_binding_sites-sorted.bed X4RG73R.bamlist.txt X4RG73R /refs/GRCh38_no_alt_GCA_000001405.15.fasta
Command error:
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 16 samples in 16 input files
[mpileup] maximum number of reads per input file set to -d 250
Work dir:
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/5c/05659ae59ee3aa400272c983cc3420
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
nextflow -log nextflow-logs/.nextflow.log run -resume main.nf --run_mode subset --dataset_id_list cluster-input-dir/manifests/dataset-manifest-remainder-rerun.txt -c nextflow_cluster.config -with-dag workflow-reports/v4/dag-20240311-11.54.html -with-report workflow-reports/v4/report-20240311-11.54.html -with-timeline workflow-reports/v4/timeline-20240311-11.54.htmla4645388ae30d76778b55d3eed46569b4e6c7739-63ed-44aa-ad25-a94feece01e0These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.